.. and the main question- what should be in mdp file of such restrained minimisation ?
Today I've done vry properly minimisation of such system in vacuum with the CG minimisator and applied disres ( above example ) with big force constant ( disres options have been defined in the minim.mdp file ). As the result I have not noticed any perturbation in the distance between two S-S atoms the distance between wich I've constrained. 2012/4/28 James Starlight <jmsstarli...@gmail.com> > Hi Francesco! > > So I must define in the current topology the disres bettwen two S atoms ( > in the below example 1 and 10 ) to apply hormonic restains > > [ distance_restraints ] > ; ai aj type index type’ low up1 up2 fac > > 1 10 1 0 1 0.18 0.20 0.22 1.0 > > to restrain this atoms within 0.2 nm. Does it correct ? Or should I use some > other disres for such task ? > > James > > > > 2012/4/28 francesco oteri <francesco.ot...@gmail.com> > >> Hi James, >> usually people run a minimization using distance restrain on the two >> atoms in order to >> make them closer. >> Then the obtained cnfiguration is used to recalculate the topology. >> >> Francesco >> >> 2012/4/28 James Starlight <jmsstarli...@gmail.com> >> >>> Dear Gromacs Users! >>> >>> I have a model of my protein wich has 4 S-S bounds in the loop regions. >>> So I want to define in topology all those four S-S linkage. >>> >>> Unfortunatelly one of that S-S have not been recognised by Gromacs ( >>> Also I've tried to check this bond in pymol and found that distance between >>> that two Cys Cys are larger for S-S occurence) due to some inaccyracy of >>> model. >>> >>> Is there any way to define such missing S-S manually? On the gromacs >>> site I've found possible sollution by means of spechbond.dat editing. I've >>> tried to increase distance between S-S atoms but this have not had >>> desirebly affect. >>> >>> In the topology.top file I've found that the S-S bonds beetween S atoms >>> are defined in the bond section without any type for such bond type. Also >>> I've found that the same enties are present in the angle and dihedralls >>> sections. Could I define the same contact only in the bond section and >>> further minimise my system to obtain new S-S linckage or should I also >>> define all other enties ( like dihedralls etc) for that bond ? >>> >>> >>> Thanks for help >>> >>> >>> James >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> >> -- >> Cordiali saluti, Dr.Oteri Francesco >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
